Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

Details

Ressource 1Download: BMCgenomic.pdf (2274.48 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_6472B5BCD4D2
Type
Article: article from journal or magazin.
Collection
Publications
Title
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.
Journal
BMC genomics
Author(s)
Bochkareva O.O., Moroz E.V., Davydov I.I., Gelfand M.S.
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Publication state
Published
Issued date
27/12/2018
Peer-reviewed
Oui
Volume
19
Number
1
Pages
965
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.
We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.
This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
Keywords
Burkholderia/classification, Burkholderia/genetics, Chromosomes, Bacterial, Databases, Genetic, Gene Rearrangement/genetics, Phylogeny, Burkholderia, Comparative genomics, Genome rearrangements, Multi-chromosome bacteria, Pan-genome, Positive selection, Strain phylogeny
Pubmed
Web of science
Open Access
Yes
Create date
17/01/2019 16:11
Last modification date
10/01/2020 18:28
Usage data